circDraw 0.0.1

A python package for circDraw visualization

circDraw

A python package for circDraw visualization

Usage

from circDraw import circDraw

 # initiate a circDraw instance
cd = circDraw()

# set color of circ_on_chr (optional)
cd.set_palette(["#5CA0F2", "#FF881D", '#e30067', '#924900','#ab9c00','#ccd0d2', '#075800', '#5e0094',])

# set color of modifications (optional)
mod_palette = {'m6a': '#E98B2A',
               'm5c': '#E16B8C',
               'm1a': '#64363C',
               'pu': '#ffa12c',
               '2ome': '#1a6f00',
               'mre': '#6D2E5B',
               'rbp': "#2B5F75",
               'orf': '#516E41'}
cd.set_mod_palette(mod_palette)

# draw backsplicing site on chromosome region
cd.circ_on_chr('Your file')

# draw modifications on circRNA
cd.mod_on_circ('Your file')

API

#####circ_on_chr

circDraw.circ_on_chr(file, title='circDraw', dpi=300, save='png', show=True, size=(10, 5))

• File:

  • Only supported 'csv'

  • Start	End	Type	Name	Color (Optional)

  • Start < End

  • Type: circ, exon, intron, gene

  • Color: RGB, RGBA, hex, or supported color names.

• Title: The title of the plot

• Save: file format you wish to save as, PNG, PDF, JPEG, etc.

• Show: Bool, wheather to show the plot after rendering.

• Size: (Length, Width) the size of the plot.

#####mod_on_circ

circDraw.mod_on_circ(self, file, dpi=100, save='png', show=True, size=(7, 7), sep_mod=False)

• File:

  • Only supported 'csv'

  • Start	End	Type	Name	Color (Optional)

  • Start < End

  • Type: circ, exon, intron, and modifications type

    • Modifications type: m6A, m1A, m5C, pU, 2OMe, MRE, RBP, ORF

  • Color: RGB, RGBA, hex, or supported color names.

• Save: file format you wish to save as, PNG, PDF, JPEG, etc.

• Show: Bool, wheather to show the plot after rendering.

• Size: (Length, Width) the size of the plot.

• sep_mod: Bool, prevent the modifications from overlapping if set True.

set_palette

circDraw.set_palette(palette)

A list of colors, the length of the list must bigger than 5.

set_mod_palette

circDraw.set_mod_palette(palette)

A dictionary of colors match with the modification. You can change any one of the modification colors.